Empty BAM after running SplitNCigarReads about gatk

[gokalpcelik]

Can you setup your temporary folder to a location where you have read and write access? Slurm might interfere with temporary files.
How to setup and use temporary folder for GATK local execution

[gokalpcelik]

Can you also post your log here as well?

[jamesemery]

@sonejilab. As @gokalpcelik the logs should be helpful to figure out what happened. Particularly at the end there should be an accounting of how many reads were filtered by what filters. Possibly something is unexpected about the read flags for the STAR aligned reads and most likely they are being filtered out by the tool. You can disable all of the reads filters using this argument --disable-tool-default-read-filters and then re-enable the ones that are relevant. Next I would check that your input files are populated and are on the same reference as the -R input that you specified in your command.

[sonejilab]

@gokalpcelik, setting tmp to a local folder on the node at runtime did the job. Thank you!